Dear Gromacs-users, I have been simulating a harmonic oscillator (two covalently bound dummy atoms) using stochastic dynamics. The average potential energy seems to be fine when I use a time step of 1 fs but when using a time step of 0.1 fs I observe extremly large potential energies -much to large to get the correct average potential energy of 1/2kT. I wonder whether there is a problem with the implemented algorithm when the timesteps are chosen too small. At least the paper on this algorithm (Mol. Sim. 1:3, 173-185) states that there is a problem when the product of time step and friction coefficient gets too small. Strangely enough the average potential energy gets significantly smaller when I use a time step of 0.1 fs but masses of about 0.1 amu for each atom. This I cannot explain since the friction coefficient is not a function of the mass. I have set t_tau to 400 ps anyway, so I suppose the friction coefficient would be pretty large anyway (does anyone know how t_tau relates to the friction coefficient exactly?).
What´s the problem with using small time steps and why can small masses alleviate this problem? Best Luther _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
